Created a special Edition class with handles exceptions, such as BioN…

…ode,

without resorting to boolean checking.

contrib/edition/bionode.py

@@ -0,0 +1,30 @@
+
+from fabric.api import *
+
+from edition import *
+import logging
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+ch = logging.StreamHandler()
+ch.setLevel(logging.DEBUG)
+# create formatter
+formatter = logging.Formatter('%(name)s %(levelname)s: %(message)s')
+# add formatter to ch
+ch.setFormatter(formatter)
+logger.addHandler(ch)
+
+class BioNode(Edition):
+    """BioNode specialization of BioLinux
+    """
+    def __init__(self, env):
+        self.name = "BioNode Edition"
+        self.env = env
+        self.include_oracle_virtualbox = False
+        self.include_freenx = False
+
+    def check_packages_source(self):
+        # Bionode removes sources, just to be sure
+        logger.debug("Clearing %s" % self.env.sources_file)
+        sudo("cat /dev/null > %s" % self.env.sources_file)
+

edition.py

@@ -1,6 +1,26 @@
+import logging
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+ch = logging.StreamHandler()
+ch.setLevel(logging.DEBUG)
+# create formatter
+formatter = logging.Formatter('%(name)s %(levelname)s: %(message)s')
+# add formatter to ch
+ch.setFormatter(formatter)
+logger.addHandler(ch)
+
 
 class Edition:
-  """Base class. Every edition derives from this
-  """
-  def __init__(self):
-    self.name = "BioLinux base Edition"
+    """Base class. Every edition derives from this
+    """
+    def __init__(self, env):
+        self.name = "BioLinux base Edition"
+        self.env = env
+        self.include_oracle_virtualbox = True
+        self.include_freenx = True
+
+    def check_packages_source(self):
+        """Override for check package definition file before updating
+        """
+        logger.debug("check_packages_source not implemented")

fabfile.py

@@ -41,7 +41,7 @@
 
 from edition import *
 
-edition = Edition()
+edition = Edition(env)  # default is empty Edition
 
 env.config_dir = os.path.join(os.path.dirname(__file__), "config")
 if not env.get('edition'):
@@ -55,19 +55,24 @@
 env.ubuntu = False       # is it pure Ubuntu?
 env.centos = False       # is it pure CentOS?
 env.deb_derived = False  # is it Debian derived?
-env.bionode = False      # is it a bionode?
 
 # ### Configuration details for different server types
+from contrib.edition.bionode import *
 
-def _setup_distribution_environment():
-    """Setup distribution environment
+def _setup_edition():
+    """Setup one of the BioLinux editions (which are derived from
+       the Edition base class)
     """
-    _parse_fabricrc()
-    logger.info("Edition %s %s" % (env.edition,env.edition_version))
+    global edition
+    logger.debug("Edition %s %s" % (env.edition,env.edition_version))
     if env.edition == 'bionode':
         env.bionode = True
-    if env.bionode:
-        logger.info("Note: this is a BioNode specialization!")
+        edition = BioNode(env)
+    logger.info("This is a %s" % edition.name)
+
+def _setup_distribution_environment():
+    """Setup distribution environment
+    """
     logger.info("Distribution %s" % env.distribution)
     if env.distribution == 'debian':
       env.debian = True
@@ -163,11 +168,12 @@ def _setup_deb_general():
     shared_sources = [
       "deb http://nebc.nox.ac.uk/bio-linux/ unstable bio-linux", # Bio-Linux
     ]
-    if not env.bionode:
-        # virtualbox (non-free, bionode uses virtualbox-ose instead)
-        shared_sources += "deb http://download.virtualbox.org/virtualbox/debian %s contrib",
+    if edition.include_oracle_virtualbox:
+        # virtualbox (non-free, otherwise use virtualbox-ose instead)
+        shared_sources.append('deb http://download.virtualbox.org/virtualbox/debian %s contrib')
+    if edition.include_freenx:
         # this arguably belongs in _setup_ubuntu:
-        shared_sources += "deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu lucid main", # FreeNX PPA
+        shared_sources.append('deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu lucid main') # FreeNX PPA
     return shared_sources
 
 def _setup_centos():
@@ -249,6 +255,8 @@ def install_biolinux(target=None):
       - finalize     Setup freenx
     """
     _check_fabric_version()
+    _parse_fabricrc()
+    _setup_edition()
     _setup_distribution_environment() # get parameters for distro, packages etc.
     pkg_install, lib_install = _read_main_config()  # read main.yaml
     _validate_target_distribution()
@@ -486,6 +494,8 @@ def install_libraries(language):
     """High level target to install libraries for a specific language.
     """
     _check_fabric_version()
+    _parse_fabricrc()
+    _setup_edition()
     _setup_distribution_environment()
     _do_library_installs(["%s-libs" % language])
 
@@ -527,10 +537,12 @@ def _add_apt_gpg_keys():
     """
     logger.info("Update GPG keys for repositories")
     standalone = [
-        "http://archive.cloudera.com/debian/archive.key",
-        "http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc"]
+        "http://archive.cloudera.com/debian/archive.key"
+    ]
+    if edition.include_oracle_virtualbox:
+        standalone.append('http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc')
     keyserver = []
-    if not env.bionode: # FIXME: should really be: if env.ubuntu:
+    if env.ubuntu:
         keyserver = [
             ("keyserver.ubuntu.com", "7F0CEB10"),
             ("keyserver.ubuntu.com", "E084DAB9"),
@@ -584,11 +596,9 @@ def _setup_apt_sources():
        Uses python-software-properties, which provides an abstraction of apt repositories
     """
     sudo("apt-get install -y --force-yes python-software-properties")
-    if env.bionode:
-      # remove sources, just to be sure
-      sudo("cat /dev/null > %s" % env.sources_file)
+    edition.check_packages_source()
 
-    comment = "# This file was modified for BioLinux"
+    comment = "# This file was modified for "+edition.name
     if not contains(env.sources_file, comment):
         append(env.sources_file, comment, use_sudo=True)
     for source in env.std_sources: